How Cerebrarium is made
The atlas and the reels start from real scans of real people, not from drawings. Here is the path from scanner to screen, and where the data come from.
The brain in the atlas
Most reels show one and the same brain: a healthy volunteer who was scanned at 7 Tesla for an open research dataset (Lüsebrink et al., Scientific Data 2021) and agreed to share the images with everyone. A hospital scanner runs at 1.5 or 3 Tesla. At 7 Tesla the images are sharp enough for voxels of 0.25 mm, each one 1/64 of the volume of a standard 1 mm voxel.
Because it is always the same person, the structures fit together from one reel to the next: the thalamus in the Papez circuit is the same thalamus as in the basal ganglia series.
From scan to model
Scan
The volunteer’s MRI and angiograms (the images that show the arteries) are downloaded from the open dataset.
Outline
Larger structures are segmented on that scan with FreeSurfer. Arteries and small channels are traced by hand. Nuclei too small for any scan, and fibre tracts, come from published atlases.
Build
Every outline becomes a 3D surface. All of them are moved into the same standard space, so each part sits where it really is relative to the others.
Film
A camera path, one lighting set-up and the colour code below turn the models into a 30 to 40 second reel. Labels and text are added last, and every fact is checked against the sources named under the video.
The 3D preview on the home page
The 3D brain on the home page uses only openly licensed data:
- Skull: a micro-CT scan of a human skull from Halle (Kirchner, 2022, CC BY 4.0), its bones fitted around the brain.
- Brain: the 7 Tesla volunteer (Lüsebrink et al. 2021, CC0): cortex and lobes, cerebellum, brainstem and most deep nuclei.
- Small midbrain nuclei: subthalamic nucleus, substantia nigra and red nucleus from the MASSP 2.0 atlas (Bazin et al. 2025, CC BY 4.0).
- Fibre tracts: the HCP1065 atlas (Yeh 2022, CC BY-SA 4.0), averaged from the diffusion scans of 1,065 people of the Human Connectome Project.
The colour code
Colours are not the real colours of brain tissue. They are a code, and every reel uses the same one, so you can recognise a structure at a glance.
| Structure | Colour |
|---|---|
| Arteries | red, satin |
| Veins and sinuses | blue |
| Ventricles and cerebrospinal fluid | cyan, with a slight glow |
| Cranial nerves | yellow |
| Fibre tracts | one colour per tract (corticospinal tract orange, optic radiation violet); the right side in a paired colour |
| Caudate nucleus | light orange |
| Putamen | red-orange |
| Thalamus | teal |
| Hippocampus | yellow |
| Lesion or problem | pulsing red glow |
| The rest of the brain | see-through glass, so you can look inside |
What is drawn by hand
Some things cannot be seen on any scan: where fibres cross, the direction of a signal, the flow of fluid, a clot, an electrode. These are drawn schematically, along published routes, and every caption says which parts are drawn.
Questions
- Is it a real brain?
- Yes. The cortex, ventricles, deep nuclei and most arteries you see are the volunteer’s own, traced from his scans; the few parts taken from other open datasets are named under each video. Atlas structures are averages of many people, placed in the same space.
- Why does a structure look smoother than on a scan?
- The surfaces are smoothed a little for display, so you see the shape and not the voxel steps. The positions are not changed.
- Can I use the videos in my teaching?
- Most reels are under a Creative Commons licence (CC BY 4.0 or CC BY-SA 4.0); each reel’s page says which. Credit “Cerebrarium (Aldo Spolaore)” and the data sources listed there.
- Is this medical advice?
- No. It is anatomy education. If you have symptoms, see a doctor; in an emergency call 112 (EU) or 911 (US).
All datasets and their licences are listed on the credits page.